[Bioperl-l] StandAloneBlast -> bl2seq case

[Peter Schattner]

Marcel van Batenburg wrote:

> I'm employing your package to align one dna sequence of fixed length
> with other sequence using blast. I used the executable bl2seq. How can
> one run this executable in a loop (so more than once) without
> being stopped by EXCEPTION message, and how can one align a dnasequence
> with less than 11 nucleotides without being confronted with the
> same EXCEPTION message?
> The bl2seq could align a dnasequence with less than
> 11 consequtive nt when one makes a dna sequence of 11 nt by adding to its
> flanks, IUPAC symbol N. The module IUPAC.pm could give me all possible
> sequences. Subsequently, one loops thru these sequences when aligning
> to a fixed second dnasequence. This will work if the excutable does not
> terminate the holy workings of my perl script due to a detected
> misalignment (alignment is according to bl2seq an aligment of more than/or
> equal to 11 consecutive basepairs).

I suspect that you are getting your exception messages from the Blast program

and not from StandAloneBlast.pm or bioperl  Do you get the exception messages

if you run bl2seq directly from the command line or from a perl script using
a 'system' call without using bioperl?  If so, bioperl probably can't help
you.

 On the other hand,  if you can run the command successfully from the command

line or using a perl system call, the problem may well be with bioperl.  To
track it down, it would be very helpful if you send in exactly what the
exception message stated as well as the perl script that caused it to happen.

Peter Schattner